| Course title | Systems Biology |
|---|---|
| Course code | KBI/SBA |
| Organizational form of instruction | Lecture |
| Level of course | Master |
| Year of study | not specified |
| Semester | Winter |
| Number of ECTS credits | 3 |
| Language of instruction | English |
| Status of course | Compulsory-optional |
| Form of instruction | Face-to-face |
| Work placements | This is not an internship |
| Recommended optional programme components | None |
| Lecturer(s) |
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| Course content |
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Lecture 1. Introduction to Systems Biology (SB) and Basic Definitions - 21.09.2023 Lecture 2. Structures, Complexity and Chaos - 5.10.2023 Lecture 3. Living Systems and Information - 12.10.2023 Lecture 4. Living Systems and Energy - 19.10.2023 Lecture 5. Living Systems and Adaptation - 26.10.2023 Lecture 6. Living Systems and Evolution - 2.11.2023 Lecture 7. Systems Biology in Plant Science - 9.11.2023 Lecture 8. Systems Biology in Medicine - 16.11.2023 Lecture 9. Systems Biology in Drug Development and Material Science - 23.11.2023 Lecture 10. Patterns in Nature - 30.11.2023 Lecture 11. Artificial Intelligence in Systems Biology - 7.12.2023 Lecture 12. Emerging Topics in Systems Biology - 14.12.2023 Topics: order; complexity; non-equilibrium systems; homeostasis; metabolism; self-sustenance and self-regulation; holism; reductionism; top-down; bottom-up; "omics"; emergence; nested hierarchy; biological robustness; systems theory; mathematical modelling; networks (graphs) theory; chaos theory; the butterfly effect; synergy; Markov chains; signals and messages; inter-and intracellular communication; 3D-bioprinting; enthalpy; entropy; Gibbs free energy; bioenergetics; phototrophy; chemotrophy; autotrophy; heterotrophy; detrivory; saprotrophy; mixotrophy; mycoheterotrophy; parasitism; endergonic vs. exergonic reactions; compartmentalization; bioluminescence; adaptations; homeostasis; allostasis; allostatic load; stress; eustress; distress; general adaptation syndrome; "fight-or-flight-or-freeze";"fight-flight"; microbiome; successions; Bergman's rule; Allen's rule; Gloger's rule; Foster's rule; latitudinal gradient; dormancy mechanisms; extremophiles; evolution theory; micro- and macroevolution; gene pool; gene flow; gene drift; bottleneck effect; founder effect; lateral (horizontal) gene transfer; conjugation; transformation; transduction; vesiduction; mutations; endosymbiosis; organellogenesis; "junk DNA"; speciation; phylogeny; taxonomy; cladistics;smart farming; plant phenotyping; drones; plant microbiome; hub microorganisms; keystone species; biofilm; quorum sensing; P4 medicine; personalized healthcare; stratified medicine; precision medicine; systems medicine; disease maps; biomarkers; exposome; translational biomedicine; cojoint analysis; orphan drugs; drug delivery systems; drug repurposing/repositioning; biomimetics; biomimicry; bionics; robotics; bio-inspired technologies; biomimetic products; aircraft; taq-polymerase; Velcro; biomimetic architecture; self-healing materials; biomimetic synthesis; artificial enzymes; nanozymes; symmetry and antisymmetry in living systems; plant axes; trees and branching patterns (ramifications); spirals (logarithmic spiral, phyllotaxis, parastichy, Fibonacci ratios, Fermat's spiral); phyllotaxis; tessellations in nature; fractals; fractal-like patterns; Mandelbrot set; geomorphology; aeolian landforms; Voronoi diagrams in developmental biology; neural networks (NN); Neocortical column; Markram's model; artificial intelligence; machine learning; deep learning; supervised and unsupervised machine learning; astrobiology (exobiology); RNA world hypothesis; space farming; seed films; Veggie; astrobotany; simulated microgravity; clinostat rotation; synthetic biology; aptamers; gene circuits; bioreporters; biosensors; Xna-xeno-DNA; Mycoplasma laboratorium or Synthia; protocells; artificial life (A-life); synthetic minimal cells; DNA nanostructures for drug delivery; DNA origami.
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| Learning activities and teaching methods |
Monologic Lecture(Interpretation, Training), Dialogic Lecture (Discussion, Dialog, Brainstorming)
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| Learning outcomes |
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The main purpose of the Systems Biology course is to explore multidisciplinarity in modern biological research. The structure of the discipline includes the integration of knowledge from the different levels of living organisms organization, the introduction of basic definitions (holism/reductionism, emergence principle, graph, chaos, information theories, multi-"omics" approach, etc.), and their implementation in various fields of biology, biomedicine and related fields (plant biology, medicine, drug design, and material science). Special attention is dedicated to emerging topics in systems biology and biology in general (e.g., synthetic biology, cell-free systems, XNA, Astro- (exo-)biology, and others) as well as to neural networks, artificial intelligence, machine, and deep learning.
Systems medicine implications in novel drug research and development. Translational biomedicine. Comparison between traditional and systems approaches to drug development. Systems pharmacology: when multi-targeting is advantageous. Phases of drug discovery and development: discovery and development; preclinical research; clinical development; review and approval. The topology-based target identification process. Conjoint analysis. The hit-effect association and prediction process. Network-based technologies for early drug discovery. Drug approval: U.S. Food and Drug Administration, European Medicines Agency, Pharmaceuticals, and Medical Devices Agency. Orphan drugs. Drug delivery systems. Hierarchy of targeted drug delivery: primary, secondary, tertiary. Drug Central and Drugmap Central. Drug repurposing/repositioning. Biomimetics, biomimicry, bionics, robotics, bio-inspired technologies. Biomimetic products and technologies: aircraft, taq-polymerase, Velcro, biomimetic architecture, self-healing materials, etc. Biomimetic synthesis. History of natural patterns study Plato, Pythagoras of Samos, Empedocles, Joseph Plateau, Ernst Haeckel, Sir D'Arcy Thompson, Alan Turing, Aristid Lindenmayer, Benoit Mandelbrot, and others. Geometrical figures and nature forms. Symmetry in living systems (bilateral/mirror; radial/rotational; fivefold; spherical) and in non-living ones (crystal habits). The different planes of bilateral symmetry: sagittal, transverse, posterior, anterior, dorsal, ventral. the order of rotational symmetry. plant axes: mediolateral; adaxial-abaxial; distal-proximal axis; descending and ascending. Trees and branching patterns (ramifications). Spirals (logarithmic spiral, phyllotaxis, parastichy, Fibonacci ratios, Fermat's spiral). Phyllotaxis as the relative positioning of new leaves: distichous, spiral (parastichous), decussate, and whorled. Asymmetry in nature and its importance. Different types of asymmetry: fluctuating asymmetry, directional asymmetry, and antisymmetry. Tessellations in nature. Fractals, fractal-like patterns, and Mandelbrot set. Voronoi diagram and tesselations. Geomorphology: aeolian landforms. Neural networks (NN): biological and artificial NN. Blue Brain Project. Neocortical column. Markram's model. Six layers of the neocortex. A theory of how columns in the neocortex enable learning the structure of the world. Artificial neural networks (ANN): definition, examples, applications, training. Artificial intelligence, machine learning, and deep learning. Supervised and unsupervised machine learning. Astrobiology (exobiology): a new horizon. Extreme environments and extremotolerant organisms. Extremophilic models for astrobiology. RNA world hypothesis. Growing plants in space (space farming), missions VEG-03I and VEG-03J, seed films, Veggie. Astrobotany: simulated microgravity and clinostat rotation. Synthetic biology: definitions and key features. The second decade of synthetic biology: 2010-2020. Top-down and bottom-up approaches in synthetic biology. Cell-free synthetic biology: engineering beyond the cell. Advantages and applications of cell-free synthetic biology. DNA nanostructures for drug delivery: "DNA-brick self-assembly" and DNA origami. CADNANO software for designing three-dimensional DNA origami nanostructures. Aptamers. Gene circuits and gene circuit engineering. Synthetic minimal cells. Protocells and artificial life (A-life). Xna-Xeno-DNA nucleic acid analogs. Bioreporters. RNA-based biosensors and synthetic biology platforms for in vitro diagnostics. Synthetic biology devices for in vivo diagnostics. Biosafety and bioethics concerns. |
| Prerequisites |
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Lecture 1. Introduction to Systems Biology (SB) and Basic Definitions - 21.09.2023 Lecture 2. Structures, Complexity and Chaos - 5.10.2023 Lecture 3. Living Systems and Information - 12.10.2023 Lecture 4. Living Systems and Energy - 19.10.2023 Lecture 5. Living Systems and Adaptation - 26.10.2023 Lecture 6. Living Systems and Evolution - 2.11.2023 Lecture 7. Systems Biology in Plant Science - 9.11.2023 Lecture 8. Systems Biology in Medicine - 16.11.2023 Lecture 9. Systems Biology in Drug Development and Material Science - 23.11.2023 Lecture 10. Patterns in Nature - 30.11.2023 Lecture 11. Artificial Intelligence in Systems Biology - 7.12.2023 Lecture 12. Emerging Topics in Systems Biology - 14.12.2023 Topics: order; complexity; non-equilibrium systems; homeostasis; metabolism; self-sustenance and self-regulation; holism; reductionism; top-down; bottom-up; "omics"; emergence; nested hierarchy; biological robustness; systems theory; mathematical modelling; networks (graphs) theory; chaos theory; the butterfly effect; synergy; Markov chains; signals and messages; inter-and intracellular communication; 3D-bioprinting; enthalpy; entropy; Gibbs free energy; bioenergetics; phototrophy; chemotrophy; autotrophy; heterotrophy; detrivory; saprotrophy; mixotrophy; mycoheterotrophy; parasitism; endergonic vs. exergonic reactions; compartmentalization; bioluminescence; adaptations; homeostasis; allostasis; allostatic load; stress; eustress; distress; general adaptation syndrome; "fight-or-flight-or-freeze";"fight-flight"; microbiome; successions; Bergman's rule; Allen's rule; Gloger's rule; Foster's rule; latitudinal gradient; dormancy mechanisms; extremophiles; evolution theory; micro- and macroevolution; gene pool; gene flow; gene drift; bottleneck effect; founder effect; lateral (horizontal) gene transfer; conjugation; transformation; transduction; vesiduction; mutations; endosymbiosis; organellogenesis; "junk DNA"; speciation; phylogeny; taxonomy; cladistics;smart farming; plant phenotyping; drones; plant microbiome; hub microorganisms; keystone species; biofilm; quorum sensing; P4 medicine; personalized healthcare; stratified medicine; precision medicine; systems medicine; disease maps; biomarkers; exposome; translational biomedicine; cojoint analysis; orphan drugs; drug delivery systems; drug repurposing/repositioning; biomimetics; biomimicry; bionics; robotics; bio-inspired technologies; biomimetic products; aircraft; taq-polymerase; Velcro; biomimetic architecture; self-healing materials; biomimetic synthesis; artificial enzymes; nanozymes; symmetry and antisymmetry in living systems; plant axes; trees and branching patterns (ramifications); spirals (logarithmic spiral, phyllotaxis, parastichy, Fibonacci ratios, Fermat's spiral); phyllotaxis; tessellations in nature; fractals; fractal-like patterns; Mandelbrot set; geomorphology; aeolian landforms; Voronoi diagrams in developmental biology; neural networks (NN); Neocortical column; Markram's model; artificial intelligence; machine learning; deep learning; supervised and unsupervised machine learning; astrobiology (exobiology); RNA world hypothesis; space farming; seed films; Veggie; astrobotany; simulated microgravity; clinostat rotation; synthetic biology; aptamers; gene circuits; bioreporters; biosensors; Xna-xeno-DNA; Mycoplasma laboratorium or Synthia; protocells; artificial life (A-life); synthetic minimal cells; DNA nanostructures for drug delivery; DNA origami.
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| Assessment methods and criteria |
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Mark, Didactic Test
Successful completion of Final Test. |
| Recommended literature |
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| Study plans that include the course |
| Faculty | Study plan (Version) | Category of Branch/Specialization | Recommended semester | |
|---|---|---|---|---|
| Faculty: Faculty of Science | Study plan (Version): Biotechnology and Genetic Engineering (2019) | Category: Chemistry courses | 1 | Recommended year of study:1, Recommended semester: Winter |